Atomistic Simulation Study of Calcium,Phosphate and Fluoride Ion Association to the Teleopeptide‐Tails of Collagen – Initial Steps to Biomineral Formation

The attachment of single ions to putative adsorption sites in the tails of collagen fibers is investigated by means of molecular dynamics simulations and discussed with respect to the very early steps of apatite/collagen biomineral formation. Our studies clearly demonstrate an increased flexibility of the tails of the triple‐helical collagen protein. Apart from the termini of the backbone, several side chains were also observed to be freely accessible to ion attachment from aqueous solution. The teleopeptide was systematically scanned for suitable adsorption sites for calcium, phosphate and fluoride ions. Association of these ions was then explored from potential of mean force calculations. The resulting energy profiles reveal a variety of favorable protein‐ion bonds and hint at the suitability of the collagen tails to promote apatite aggregation.     

Application of isotopic labeling,and gas chromatography mass spectrometry,to understanding degradation products and pathways in the thermal-oxidative aging of Nylon 6.6

Nylon 6.6 containing ¹³C isotopic labels at specific positions along the macromolecular backbone has been subjected to extensive thermal-oxidative aging at 138 °C for time periods up to 243 days. In complementary experiments, unlabeled Nylon 6.6 was subjected to the same aging conditions under an atmosphere of ¹⁸O₂. Volatile organic degradation products were analyzed by cryofocusing gas chromatography mass spectrometry (cryo-GC/MS) to identify the isotopic labeling. The labeling results, combined with basic considerations of free radical reaction chemistry, provided insights to the origin of degradation species, with respect to the macromolecular structure. A number of inferences on chemical mechanisms were drawn, based on 1) the presence (or absence) of the isotopic labels in the various products, 2) the location of the isotope within the product molecule, and 3) the relative abundance of products as indicated by large differences in peak intensities in the gas chromatogram. The overall degradation results can be understood in terms of free radical pathways originating from initial attacks on three different positions along the nylon chain which include hydrogen abstraction from: the (CH₂) group adjacent to the nitrogen atom, at the (CH₂) adjacent the carbonyl group, and direct radical attack on the carbonyl. Understanding the pathways which lead to Nylon 6.6 degradation ultimately provides new insight into changes that can be leveraged to detect and reduce early aging and minimize problems associated with material degradation.     

Atomic mechanisms of superionic conductivity in fluorite

The subsequent melting/crystallization of the two sub-lattices of CaF₂ is explored by molecular dynamics simulations. Both, heating from 100 K and cooling from 2500 K encompasses two transitions, i.e. the melting/recrystallization of the fluoride sub-lattice and the of whole crystal at different temperatures. Solid state F^? ion conductivity is observed in a temperature range of about 1500–2000 K which reflects a reasonable agreement with the experiment. A systematic study of fluoride migration revealed the atomistic mechanisms of the spontaneous formation of Frenkel defects, followed by void translocation and terminated by recombination of interstitial fluoride ions and vacancies.     

PROCOS: computational analysis of protein-protein complexes

One of the main challenges in protein-protein docking is a meaningful evaluation of the many putative solutions. Here we present a program (PROCOS) that calculates a probability-like measure to be native for a given complex. In contrast to scores often used for analyzing complex structures, the calculated probabilities offer the advantage of providing a fixed range of expected values. This will allow, in principle, the comparison of models corresponding to different targets that were solved with the same algorithm. Judgments are based on distributions of properties derived from a large database of native and false complexes. For complex analysis PROCOS uses these property distributions of native and false complexes together with a support vector machine (SVM). PROCOS was compared to the established scoring schemes of ZRANK and DFIRE. Employing a set of experimentally solved native complexes, high probability values above 50% were obtained for 90% of these structures. Next, the performance of PROCOS was tested on the 40 binary targets of the Dockground decoy set, on 14 targets of the RosettaDock decoy set and on 9 targets that participated in the CAPRI scoring evaluation. Again the advantage of using a probability-based scoring system becomes apparent and a reasonable number of near native complexes was found within the top ranked complexes. In conclusion, a novel fully automated method is presented that allows the reliable evaluation of protein-protein complexes.     

DNA localization and stretching on periodically microstructured lipid membranes

We study the conformational behavior of DNA molecules adsorbed on cationic-lipid membranes that are supported on grooved, one-dimensionally periodic microstructured surfaces. We reveal a striking ability of these periodically structured membranes to stretch DNA coils. We elucidate this DNA stretching phenomenon in terms of surface curvature dependent potential energy attained by the adsorbed DNA molecules. Because of it, DNA molecules undergo a localization transition causing them to stretch by binding to highly curved sections of the supported membranes.     

LiSr2[ReN4] und LiBa2[ReN4] – isotype Nitridorhenate(VII)

LiSr₂[ReN₄] and LiBa₂[ReN₄] – isotypic Nitridorhenates(VII) The quaternary nitridorhenates(VII) LiAE₂[ReN₄] (AE = Sr, Ba) were synthesized by reaction of the metals with molecular nitrogen at 850–900 °C. The plate‐like, nearly colourless crystals were investigated by X‐ray single crystal methods and were identified as isotypic phases: LiSr₂[ReN₄] (LiBa₂[ReN₄]); monoclinic, P2₁/m; a = 614.64(8) pm (651.04(12) pm), b = 585.97(6) pm (b = 598.86(9) pm), c = 689.70(17) pm (737.43(5) pm), β = 106.375(4)° (108.535(2)°); Z = 2. Crystals of the strontium compound were systematically twinned along [001]. In the crystal structures of the quaternary compounds the alkaline earth‐ and nitride‐ ions are arranged in the motif of the InNi₂‐type structure. Strontium and barium are in a trigonal prismatic coordination by nitrogen (Sr–N: 261.0(7)–284.3(4) pm; Ba–N: 278.0(7)–303.0(6) pm). One half of the tetrahedral voids within the partial structure formed by stacking of trigonal prismatic rod layers is occupied by rhenium (formation of [Re^VIIN₄]^5–‐tetrahedra; Re–N: 181.0(6)–184.5(8) pm), lithium takes the positions of the remaining tetrahedral sites (Li–N: 2 × 198(1) pm, 224(2) pm and 228(2) pm for the strontium phase). In the barium compound the lithium positions show a larger shift from the tetrahedral centres towards a tetrahedral plane (Li–N: 2 × 195(1) pm, 213(2) pm and 304(2) pm).     

CONTROLLING THE 3D NANOSCALE ORGANIZATION OF BULK HETEROJUNCTION POLYMER SOLAR CELLS

In this study,the three dimensional nanoscale organization in the photoactive layers of poly(3-hexylthiophene) (P3HT) and a methanofullerene derivative (PCBM) is revealed by transmission electron tomography.After annealing treatment,either at elevated temperature or during slow solvent evaporation,nanoscale interpenetrating networks are formed with high crystalline order and favorable concentration gradients of both components through the thickness of the photoactive layer.Such a tailored morphology acco...     

Structure and mobility of lipid membranes on a thermoplastic substrate

Supported lipid membranes constitute one of the most important model systems for cell membranes. The properties of lipid membranes supported by the hydrophobic solid polymer cyclic olefin copolymer (COC) were investigated. Lipid layers consisting of varying amounts of 1,2-dioleoyl-3-trimethylammonium propane (DOTAP, cationic) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC, neutral) prepared by vesicle fusion and solvent exchange were compared. All lipid mixtures coated the COC surface homogeneously forming a fluid membrane as verified by fluorescence microscopy and fluorescence recovery after photobleaching (FRAP). The exact structure of the supported membranes was determined by synchrotron reflectivity experiments using a microfluidic chamber. The X-ray data are in agreement with a compressed (head-to-head distance = 29 angstroms) and less densely packed bilayer.